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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT OF AN INTERNATIONAL MARKER ASSISTED SELECTION PROGRAM FOR CACAO

Location: Subtropical Horticulture Research

Title: Cocoa/Cotton Comparative Genomics

Authors
item May, Gregory -
item Mudge, Joann -
item Crow, John -
item Bharti, Arvind -
item Woodward, Jimmy -
item Ramaraj, Thiru -
item Farmer, Andrew -
item Rice, Brandon -
item Kramer, Robin -
item Wilkins, Thea -
item Schmutz, Jeremy -
item Kim, Ryan -
item Mockaitis, Keithanne -
item Saski, Chris -
item Scheffler, Brian
item Main, Dorrie -
item Jenkins, Jerry -
item Livingstone, Donald
item Zheng, Ping -
item Gilbert, Don -
item Feltus, Alex -
item Haiminen, Niina -
item Parida, Laxmi -
item Tondo, Cecile
item Royaert, Stefan
item Phillips, Wilbert -
item Shapiro, Howard -
item Schnell Ii, Raymond
item Kuhn, David
item Motamayor, Juan -

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 16, 2011
Publication Date: January 16, 2011
Citation: ay, G.D., Mudge, J., Crow, J.A., Bharti, A.K., Woodward, J.E., Ramaraj, T., Farmer, A.D., Rice, B.J., Kramer, R.S., Wilkins, T.A., Schmutz, J., Kim, R.W., Mockaitis, K., Saski, C., Scheffler, B.E., Main, D., Jenkins, J., Livingstone, D., Zheng, P., Gilbert, D., Feltus, A., Haiminen, N., Parida, L., Tondo, C.L., Royaert, S.E., Phillips, W., Shapiro, H., Schnell, R.J., Kuhn, D.N., Motamayor, J. 2011. Cocoa/Cotton Comparative Genomics. Annual International Plant & Animal Genome Conference. 2011.

Interpretive Summary: Theobroma cacao, the source of cocoa beans for chocolate, is an important tropical agriculture commodity that is affected by a number of fungal pathogens and insect pests, as well as concerns about yield and quality. We are trying to find molecular genetic markers that are linked to disease resistance and other important economic traits to aid in a marker assisted selection (MAS) breeding program for cacao to ensure a reliable supply of cocoa for the US confectionary industry. With genome sequence from two members of the Malvaceae family recently made available, we are exploring syntenic relationships, gene content, and evolutionary trajectories between the cacao and cotton genomes. Genomes of these species will synergistically aid one another both in assembly and biological analysis. Gene content differences and interruptions in synteny will allow us to trace evolutionary trajectories and focus in on important species specific traits in cotton and cacao. Genomic similarities of these two important agronomic crops will allow us to explore the overlapping set of physical and biological challenges that cotton and cacao endure such as disease resistance. Tackling these issues and applying biological knowledge across both genomes will enhance our ability to improve these crops. Our results are important to scientists trying to understand the mechanism of disease resistance and, eventually, to cacao farmers who will benefit from superior disease resistant and more productive cultivars produced through our MAS breeding program.

Technical Abstract: With genome sequence from two members of the Malvaceae family recently made available, we are exploring syntenic relationships, gene content, and evolutionary trajectories between the cacao and cotton genomes. An assembly of cacao (Theobroma cacao) using Illumina and 454 sequence technology yielded nearly 35,000 gene models with over 90% of the genome contained in 10 supercontigs. Likewise, genome sequence is available for the cotton A (Gossypium arboreum) and D genomes (G. raimondii) and for an ancestral cotton species (Gossypioides kirkii). Comparisons of the G. kirkii and cotton sequences and assemblies to the cacao physical map and genome will be made. Genomes of these species will synergistically aid one another both in assembly and biological analysis. Gene content differences and interruptions in synteny will allow us to trace evolutionary trajectories and focus in on important species specific traits in cotton and cacao. Genomic similarities of these two important agronomic crops will allow us to explore the overlapping set of physical and biological challenges that cotton and cacao endure. Tackling these issues and applying biological knowledge across both genomes will enhance our ability to improve these crops. The ability to work across species is especially important for cotton because its agronomic exploitation has led to a reduction in genetic diversity. Together the two genomes represent an important leap forward for cacao and cotton as well as other members of the Malvaceae.

Last Modified: 8/21/2014